Treeview images can be used to provide a graphical depiction of aCGH data and allow
each cDNA/gene on the microarray to be viewed in the order in which it occurs in
the genome. For viewing of aCGH data using Treeview we have found the following
parameters to work very well.
Load file (e.g., cdt file that comprises Table S4) by first opening Treeview and
going to Load to select the desired file. For large files there will be a delay of
about 10 seconds before it opens. After the .cdt file is opened in Treeview, the
default parameters can be adjusted as follows:
1. Go to Settings then select Options, then within Options, select Display.
2. In the Thumbnail image settings, make the X axis pixel size 10 and the Y axis
pixel size 1
3. In the Zoom image settings, use 12 for both the X and Y axis settings.
4. In the Contrast image settings, make the Image contrast 1.6 and the mask value
setting zero. Click on apply.
5. Go back and open Settings again, then Options, and then Colors. Click on the
"Missing" box and, in the Color window that opens, click on the “define custom
colors” box. Place the cursor on the arrow on the sliding color scale on the right,
and slide the arrow downward so that the "red, green, blue" color values are
between 60 and 65 to make the color a slightly darker gray. Then click on OK, and
then Apply.
Using the cursor, one can highlight a region (i.e. make a yellow box) in the
thumbnail image that can then be viewed in greater detail in the zoom image.
The descriptive information (text) to the right of each cDNA in the zoomed image is
hypertext-linked to the Stanford SOURCE database (which is linked to outside
databases, e.g. Golden Path, NCBI, etc.), so that one can immediately obtain
information about each cDNA/gene. In order to use this hypertext feature in
Treeview go to Settings, then Options and select Edit URL Strings. An empty box
will appear. The following URL strings should be copied and pasted into the box.
YORF=http://genome-www.stanford.edu/cgi-bin/dbrun/SacchDB?find+Locus+%22UNIQID%22
MCLID=http://genome.rtc.riken.go.jp/cgi-bin/getseq?g+R+UNIQID
CLID=http://genome-www5.stanford.edu/cgi-bin/SMD/source/sourceResult?option=CloneID&criteria1=UNIQID&choice=Gene&local=1
ACC=http://genome-www5.stanford.edu/cgi-bin/SMD/source/sourceResult?option=Number&criteria=UNIQID&choice=Gene&local=1